Tissue resolved, gene structure refined equine transcriptome

T. A. Mansour, E. Y. Scott, Carrie J Finno, Rebecca Bellone, M. J. Mienaltowski, Cecilia Penedo, P. J. Ross, S. J. Valberg, J. D. Murray, Charles Brown

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. Results: This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. Conclusions: We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.

Original languageEnglish (US)
Article number103
JournalBMC Genomics
Volume18
Issue number1
DOIs
StatePublished - Jan 20 2017

Fingerprint

Transcriptome
Horses
Genes
Protein Isoforms
Untranslated Regions
Gene Expression
Genome
RNA
Sensitivity and Specificity

Keywords

  • Equine transcriptome
  • RNA-seq
  • Tissue-specificity

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Tissue resolved, gene structure refined equine transcriptome. / Mansour, T. A.; Scott, E. Y.; Finno, Carrie J; Bellone, Rebecca; Mienaltowski, M. J.; Penedo, Cecilia; Ross, P. J.; Valberg, S. J.; Murray, J. D.; Brown, Charles.

In: BMC Genomics, Vol. 18, No. 1, 103, 20.01.2017.

Research output: Contribution to journalArticle

Mansour, TA, Scott, EY, Finno, CJ, Bellone, R, Mienaltowski, MJ, Penedo, C, Ross, PJ, Valberg, SJ, Murray, JD & Brown, C 2017, 'Tissue resolved, gene structure refined equine transcriptome', BMC Genomics, vol. 18, no. 1, 103. https://doi.org/10.1186/s12864-016-3451-2
Mansour, T. A. ; Scott, E. Y. ; Finno, Carrie J ; Bellone, Rebecca ; Mienaltowski, M. J. ; Penedo, Cecilia ; Ross, P. J. ; Valberg, S. J. ; Murray, J. D. ; Brown, Charles. / Tissue resolved, gene structure refined equine transcriptome. In: BMC Genomics. 2017 ; Vol. 18, No. 1.
@article{f44f81eb29e94cabafd9bcb316f9c954,
title = "Tissue resolved, gene structure refined equine transcriptome",
abstract = "Background: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. Results: This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. Conclusions: We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.",
keywords = "Equine transcriptome, RNA-seq, Tissue-specificity",
author = "Mansour, {T. A.} and Scott, {E. Y.} and Finno, {Carrie J} and Rebecca Bellone and Mienaltowski, {M. J.} and Cecilia Penedo and Ross, {P. J.} and Valberg, {S. J.} and Murray, {J. D.} and Charles Brown",
year = "2017",
month = "1",
day = "20",
doi = "10.1186/s12864-016-3451-2",
language = "English (US)",
volume = "18",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Tissue resolved, gene structure refined equine transcriptome

AU - Mansour, T. A.

AU - Scott, E. Y.

AU - Finno, Carrie J

AU - Bellone, Rebecca

AU - Mienaltowski, M. J.

AU - Penedo, Cecilia

AU - Ross, P. J.

AU - Valberg, S. J.

AU - Murray, J. D.

AU - Brown, Charles

PY - 2017/1/20

Y1 - 2017/1/20

N2 - Background: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. Results: This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. Conclusions: We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.

AB - Background: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. Results: This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. Conclusions: We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.

KW - Equine transcriptome

KW - RNA-seq

KW - Tissue-specificity

UR - http://www.scopus.com/inward/record.url?scp=85010934611&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85010934611&partnerID=8YFLogxK

U2 - 10.1186/s12864-016-3451-2

DO - 10.1186/s12864-016-3451-2

M3 - Article

C2 - 28107812

AN - SCOPUS:85010934611

VL - 18

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 103

ER -